If I had to make changes to the movie, they would mostly be changes that add things to the movie.
After Twilight explains her plan to the princesses, we get a short bit with Shining Armour delivering a report that most of the guards will be off-duty for the celebration. We get some stuff establishing that Shining Armour and Cadence are married, that he and Twilight are related, and that Twilight doesn’t live in Canterlot.
The other princesses have to be defeated in order for the story to work, but I’d have liked it if Canterlot had put up more of a resistance. We get a better sense that the Storm Guard’s sheer size and magic-resistant gear leaves the Royal Guard hopelessly outmatched.
Then basically don’t change anything until The Mane Six have to leave the airship. Instead of Twilight, it should be Applejack who has the idea to create the balloon. She tells everyone to trust her, which would be a nice callback to the second episode. Then, she uses her rope skills to make the balloon.
We get a better sense of Seaquestria. Just enough to get a sense of what day-to-day life is like. Twilight still tries to steal the pearl, and The Mane Six still get kicked out.
Just as a quick side note, I thought Capper was given enough character development, but Celaeno and Skystar really weren’t. So I would have it so that Skystar convinces a small detachment of volunteers to come with her. This would give us a sense of what the hippogriffs actually think about living underwater. We could even get some lines like “Anything beats being cooped up in that cave.” or “We already let our own home fall, we won’t let the same thing happen to yours.”. It would also give Skystar more depth; where her more responsible and experienced mother uses her authority to keep her species safe, the more naive and inexperienced princess instead wants to help others. It gives us a nice power play between the queen and the princess. It would also actually explain how they got back to Canterlot.
I would also have them actually formulate a plan. Maybe Celaeno has past military experience, and working for The Storm King means she knows the how to avoid patrol routes. She recognizes that The Storm Guard are overspecialized against unicorns, and the hippogriffs can drop rocks on them or something.
I’d keep the climax mostly the same, but with more hippogriffs. Also, the scene with Fluttershy was great, but I’d cut back to her to find that it’s expanded into a group therapy session. With that, each of The Mane Six has gotten to shine in some way.